Skip to content

Latest commit

 

History

History
110 lines (59 loc) · 3.53 KB

.deploy.md

File metadata and controls

110 lines (59 loc) · 3.53 KB
Raw

Deployment

Update pyproject.toml with the contents of requirements.txt

Used the following to investigate whether or not the requirements are satsified globally.

# --prefix=your/.venv

# TMPDIR=/your/choice


# pip install --isolated 

pip install --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache -r requirements.txt --dry-run

#----------------------------------------
# Build-chain
pip install setuptools>=61.0 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
pip install  wheel  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
pip install numpy>=1.22.0  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
#pip install build>=0.9.0?  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run

# Fixed #(? #3/31/24 also still out of wack, had been using a more modern toolchain for essentially no-reason. hold up)
distlib>=0.3.8 # 3/31/24 -  May need downgrade due to setuptools, build, or distlib compatibility layers under pip
Cython>=3.0.8 #?  3/31/24  - same issue. needlessly restrictive, some issues in build system prevent good correspondence with compatibility as either a conda toolchain/buildchain or a pypi module. still needs fix.


pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run

# I think build and distlib are used for Cythonization of the Pearson correlation coefficient
# I think setuptools is a Python PyPI compatibility layer for dependency layer.







#----------------------------------------
# module reqrmtx

# biopython
biopython>=1.81
pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run

# --------------- docutils
docutils>=0.17
#docutils==0.18.1
pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run

# # -------------- Sphinx
# # 3/31/24 - May need a version bump
sphinx>=4.3.2

#sphinxcontrib-htmlhelp>=2.0.0
#sphinxcontrib-serializinghtml>=1.1.5

# # 3/31/24 - Also needs a version fix. This is live i think.
#sphinx-rtd-theme>=1.0.0


## Um hs do these all need version bumps


# # Graphics

pip install matplotlib>=3.8.2 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
# # Scientific computing

#########################################
pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
pip install  pandas>=2.2.0  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run


#########################################
# Configurations


# gtfh
# # 3/31/24 needs a downgrade too
pip install PyYAML>=6.0.1 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
pip install  jsonschema>=4.21.1  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run



psutil>=5.9.8
pip install psutil>=5.9.8 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
3/31/24

Version downgrades and optionals.

biopython 1.8.3->1.81

Testing alternate install/build system.